Conventional methods and systems for fermenting and or enzymatically processing carbohydrates such as grains to produce products such as ethanol generally involve producing steam with a fire tube boiler and heating the grain or carbohydrates with steam while in the presence of enzymes, which convert the carbohydrates to sugars, and yeast or bacteria that convert the sugars to ethanol and carbon dioxide. This process is carried out in the absence of oxygen. Similarly, non-carbohydrate derived sugars such as xylose can be converted to ethanol and carbon dioxide while in the presence of yeast. The exhaust product generated from the fire tube boiler contains various nitrogen and sulfur based oxides (NOx and SOx) that may be removed via a scrubber or are exhausted to the atmosphere. Due to environmental regulations, removal of a portion of the NOx and SOx present in the exhaust may be required in some areas.